Hi Bert
Erik and Ian partly answered this, but it is always worth remembering
that SNOMED CT, if based on proper ontological principles, contains
assertions that represent entities in the real world. This means
taxonomy (IS-A) and properties, qualities, possible relationships and so
on (see BFO2
<https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjkjrG8hrTMAhWEWxQKHc_dDsIQFggcMAA&url=https%3A%2F%2Fbfo.googlecode.com%2Fsvn%2Ftrunk%2Fdocs%2Fbfo2-reference%2FBFO2-Reference.docx&usg=AFQjCNFaciudhkU555FkqpQscrO0rRJUmQ&sig2=wWITHga_L6Vp1RTU4lvEEw&bvm=bv.120853415,d.d24>for
a modern top-level ontology providing these ideas). These are
properties, qualities and relationships of real things in the real
world, i.e. actual hearts, cardiac arrests, disease types and so on.
The openEHR RM and derivative archetypes are built to represent
information 'about' these real things. The relationship is often written
as 'is-about'. There are important differences to be aware of:
* what information is written 'about' many things can sometimes
resemble a description of the thing itself, e.g. parts of a
colonoscopy report tend to follow anatomical structure of colon and
things found in it;
* sometimes it relates to a surrogate phenomenon, e.g. an archetype
for heart rate that actually records pulse; a great deal of clinical
observation is of surrogates e.g. state of skin, palpation, heart
sounds, asking about pain, blood glucose etc, but they are actually
about something else;
* what gets recorded can be what is cheap and painless to record;
consider that we don't do an echocardiogram every time you want
simple BP or heart rate.
* what gets recorded about X can be culturally determined; different
in other ways from 'how X really is' in nature.
* most important: most clinical data recordings don't replicate
'textbook' relationships found in an ontology, e.g. the fact that
there are 5 heart Korotkoff sounds at different phases of the
cardiac cycle will never be written down by a physician, neither
will the fact that systolic BP is-a pressure of blood in a vessel
is-a pressure of fluid in a vessel etc. So if we were to generate an
information structure from part of an ontology representing the
heart / CV system, it would generate numerous useless data points
and relationships on the information side.
How well or how much SNOMED CT follows underlying ontologies like BFO2
or Biotoplite or whatever is another question. I am not up to date on
the progress, but I am fairly sure that most of SNOMED has not been
validated against these kinds of ontologies. The waters are muddied
further by the attempts to represent informational, timing and
context-related entities in SNOMED CT.
Thus, my view is that: in principle, generating information structures
straight from an ontology (even a perfectly built one) will simply never
work, for the reasons in the list above; in practice, what you would get
from SNOMED CT, given its imperfect adherence to ontology would be even
harder to understand or use.
- thomas
On 29/04/2016 07:50, Bert Verhees wrote:
Hi,
I got an idea when reading the nice story from Heather on LinkedIn. In
fact it is hers idea, but in a opposing way.
https://www.linkedin.com/pulse/journey-interoperability-part-i-heather-leslie
https://www.linkedin.com/pulse/journey-interoperability-part-ii-heather-leslie
I wonder in how far it is feasible and useful to create archetypes
from SNOMED concepts, it would be possible to generate them, with
attributes and so on.
In a few hours time, one would have a complete forest with archetypes,
including ontology in more languages.
Maybe some smart handling, filtering, combining can create a better
collection, also looking at the paths, so that there are similar paths
for similar situations, to keep the number of different datapoints
low, which can help creating a faster key-value storage.
I don't know how it is about copyright, with members, and licensing,
that should be looked at.
The argument that SNOMED is fragmented should not count, I think
(however without having an expertise on this), because, when working
with handwritten archetypes will always be incomplete and fragmented.
Bert
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